Summary of WES dataset
Mafe Senosain
2021-03-12
Pre-processing of the data
## -Validating
## --Non MAF specific values in Variant_Classification column:
## Unknown
## --Non MAF specific values in Variant_Type column:
## MNP
## -Silent variants: 5466
## -Summarizing
## --Possible FLAGS among top ten genes:
## TTN
## MUC16
## USH2A
## FLG
## -Processing clinical data
## --Missing clinical data
## -Finished in 1.359s elapsed (1.307s cpu)MAF object
## An object of class MAF
## ID summary Mean Median
## 1: NCBI_Build NA NA NA
## 2: Center NA NA NA
## 3: Samples 57 NA NA
## 4: nGenes 7980 NA NA
## 5: Frame_Shift_Del 594 10.421 5
## 6: Frame_Shift_Ins 140 2.456 1
## 7: In_Frame_Del 134 2.351 1
## 8: In_Frame_Ins 21 0.368 0
## 9: Missense_Mutation 13065 229.211 104
## 10: Nonsense_Mutation 1099 19.281 7
## 11: Nonstop_Mutation 19 0.333 0
## 12: Splice_Site 3 0.053 0
## 13: total 15075 264.474 120## Warning in titv(maf = maf, useSyn = TRUE, plot = FALSE): Non standard Ti/Tv
## class: 581TRUE
Oncoplots
Transition and Transversions
## Warning in titv(maf = laml, plot = FALSE, useSyn = TRUE): Non standard Ti/Tv
## class: 581TRUE
KRAS mutations
## 2 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.## HGNC refseq.ID protein.ID aa.length
## 1: KRAS NM_004985 NP_004976 188
## 2: KRAS NM_033360 NP_203524 189## Using longer transcript NM_033360 for now.
## Assuming protein change information are stored under column AAChange. Use argument AACol to override if necessary.
## 2 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.## HGNC refseq.ID protein.ID aa.length
## 1: KRAS NM_004985 NP_004976 188
## 2: KRAS NM_033360 NP_203524 189## Using longer transcript NM_033360 for now.
Compare mutation load against TCGA cohorts
## Warning in FUN(X[[i]], ...): Removed 0 samples with zero mutations.## Performing pairwise t-test for differences in mutation burden..
Somatic Interactions
## gene1 gene2 pValue oddsRatio 00 11 01 10 Event
## 1: ERICH3 ZFHX4 1.003317e-05 32.8729364 41 9 5 2 Co_Occurence
## 2: TP53 CSMD3 1.018220e-05 19.8465407 36 12 5 4 Co_Occurence
## 3: PCDH15 OBSCN 1.388620e-05 33.4543447 43 8 3 3 Co_Occurence
## 4: CSMD3 ZFHX4 1.653064e-05 20.7539826 37 11 3 6 Co_Occurence
## 5: MUC16 CACNA1E 4.762487e-05 21.3778707 37 10 2 8 Co_Occurence
## ---
## 296: RELN CSMD1 1.000000e+00 0.9150065 37 2 9 9 Mutually_Exclusive
## 297: RYR3 OBSCN 1.000000e+00 1.0545483 38 2 9 8 Co_Occurence
## 298: RYR3 PCDH15 1.000000e+00 1.0545483 38 2 9 8 Co_Occurence
## 299: RYR3 CCDC168 1.000000e+00 1.2143645 39 2 8 8 Co_Occurence
## 300: VCAN MUC12 1.000000e+00 1.2143645 39 2 8 8 Co_Occurence
## pair event_ratio
## 1: ERICH3, ZFHX4 9/7
## 2: CSMD3, TP53 12/9
## 3: OBSCN, PCDH15 8/6
## 4: CSMD3, ZFHX4 11/9
## 5: CACNA1E, MUC16 10/10
## ---
## 296: CSMD1, RELN 2/18
## 297: OBSCN, RYR3 2/17
## 298: PCDH15, RYR3 2/17
## 299: CCDC168, RYR3 2/16
## 300: MUC12, VCAN 2/16Detecting cancer driver genes based on positional clustering
## Warning in oncodrive(maf = laml, AACol = "Protein_Change", minMut = 5,
## pvalMethod = "zscore"): Oncodrive has been superseeded by OncodriveCLUSTL. See
## http://bg.upf.edu/group/projects/oncodrive-clust.php## Estimating background scores from synonymous variants..## Not enough genes to build background. Using predefined values. (Mean = 0.279; SD = 0.13)## Estimating cluster scores from non-syn variants..##
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|======================================================================| 100%## Comapring with background model and estimating p-values..## Done !| Hugo_Symbol | Frame_Shift_Del | Frame_Shift_Ins | In_Frame_Del | In_Frame_Ins | Missense_Mutation | Nonsense_Mutation | Nonstop_Mutation | Splice_Site | total | MutatedSamples | AlteredSamples | clusters | muts_in_clusters | clusterScores | protLen | zscore | pval | fdr | fract_muts_in_clusters |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| KRAS | 0 | 0 | 0 | 0 | 24 | 0 | 0 | 0 | 24 | 24 | 24 | 2 | 22 | 0.9044628 | 189 | 4.8112522 | 0.0000007 | 0.0000180 | 0.9166667 |
| EPB41L3 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 5 | 4 | 4 | 2 | 4 | 0.8000000 | 1087 | 4.0076923 | 0.0000307 | 0.0003679 | 0.8000000 |
| EGFR | 0 | 0 | 7 | 1 | 9 | 0 | 0 | 0 | 17 | 12 | 12 | 2 | 11 | 0.5311959 | 1210 | 1.9399684 | 0.0261918 | 0.2095341 | 0.6470588 |
| ATR | 1 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 5 | 4 | 4 | 1 | 2 | 0.4000000 | 2644 | 0.9307692 | 0.1759865 | 0.4692973 | 0.4000000 |
| C8A | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 5 | 4 | 4 | 1 | 2 | 0.4000000 | 584 | 0.9307692 | 0.1759865 | 0.4692973 | 0.4000000 |
| DLGAP2 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 5 | 4 | 4 | 1 | 2 | 0.4000000 | 975 | 0.9307692 | 0.1759865 | 0.4692973 | 0.4000000 |
Clinical enrichment analysis
## Sample size per factor in Hist_predominant:##
## acinar lepidic micropapillary mucinous acinar papillary
## 26 1 7 3 6
## solid
## 14## Sample size per factor in X8th_ed_path_stage:##
## Stage IA1 Stage IA2 Stage IA3 Stage IB Stage IIA Stage IIB Stage IIIA
## 5 8 12 8 12 10 1
## Stage IIIB
## 1## Sample size per factor in n_op1:##
## agg ind
## 44 13## Sample size per factor in n_op2:##
## agg ind int
## 36 5 16## Hugo_Symbol Group1 Group2 n_mutated_group1 n_mutated_group2
## 1: KNDC1 solid Rest 7 of 14 1 of 43
## 2: CSMD3 acinar Rest 2 of 26 15 of 31
## 3: DNAH8 solid Rest 6 of 14 2 of 43
## 4: CACNA1C solid Rest 5 of 14 1 of 43
## 5: SPTA1 acinar Rest 0 of 26 9 of 31
## 6: MUC5B micropapillary Rest 4 of 7 3 of 50
## 7: FAT3 solid Rest 6 of 14 3 of 43
## 8: SPTA1 solid Rest 6 of 14 3 of 43
## 9: PAPPA2 micropapillary Rest 4 of 7 4 of 50
## 10: BRINP3 acinar Rest 0 of 26 8 of 31
## 11: ZFHX4 micropapillary Rest 5 of 7 9 of 50
## 12: LRP2 solid Rest 5 of 14 2 of 43
## 13: STAB2 solid Rest 5 of 14 2 of 43
## 14: ADGRL3 acinar Rest 1 of 26 10 of 31
## 15: OBSCN acinar Rest 1 of 26 10 of 31
## 16: PCLO micropapillary Rest 4 of 7 5 of 50
## 17: CCDC168 solid Rest 6 of 14 4 of 43
## 18: ZFHX4 acinar Rest 2 of 26 12 of 31
## 19: PKHD1L1 acinar Rest 0 of 26 7 of 31
## 20: TP53 solid Rest 8 of 14 8 of 43
## 21: USH2A micropapillary Rest 5 of 7 11 of 50
## 22: CCDC168 acinar Rest 1 of 26 9 of 31
## 23: MUC12 acinar Rest 1 of 26 9 of 31
## 24: MALRD1 solid Rest 5 of 14 3 of 43
## 25: PRDM9 solid Rest 5 of 14 3 of 43
## 26: ZAN solid Rest 5 of 14 3 of 43
## 27: CSMD3 solid Rest 8 of 14 9 of 43
## 28: ERICH3 solid Rest 6 of 14 5 of 43
## 29: OBSCN solid Rest 6 of 14 5 of 43
## 30: PLXNA4 micropapillary Rest 3 of 7 3 of 50
## 31: TMEM132B micropapillary Rest 3 of 7 3 of 50
## 32: CSMD3 micropapillary Rest 5 of 7 12 of 50
## 33: MUC16 acinar Rest 4 of 26 14 of 31
## 34: TTN solid Rest 8 of 14 10 of 43
## 35: CACNA1C acinar Rest 0 of 26 6 of 31
## 36: TENM3 acinar Rest 0 of 26 6 of 31
## 37: MYH6 acinar Rest 0 of 26 6 of 31
## 38: TSHZ3 acinar Rest 0 of 26 6 of 31
## 39: ZNF479 acinar Rest 0 of 26 6 of 31
## 40: MUC5AC acinar Rest 0 of 26 6 of 31
## 41: EGFR acinar Rest 9 of 26 3 of 31
## 42: ZFHX4 solid Rest 7 of 14 7 of 43
## 43: FLG solid Rest 7 of 14 7 of 43
## 44: COL6A5 solid Rest 4 of 14 2 of 43
## 45: MROH2B solid Rest 4 of 14 2 of 43
## 46: SALL3 solid Rest 4 of 14 2 of 43
## 47: UNC79 solid Rest 4 of 14 2 of 43
## 48: ANK3 solid Rest 4 of 14 2 of 43
## 49: TENM3 solid Rest 4 of 14 2 of 43
## 50: MYH6 solid Rest 4 of 14 2 of 43
## 51: TSHZ3 solid Rest 4 of 14 2 of 43
## 52: ZNF479 solid Rest 4 of 14 2 of 43
## 53: BECN2 solid Rest 4 of 14 2 of 43
## 54: EGFLAM solid Rest 4 of 14 2 of 43
## 55: GRIK4 solid Rest 4 of 14 2 of 43
## 56: GRIN2B solid Rest 4 of 14 2 of 43
## 57: MUC5AC solid Rest 4 of 14 2 of 43
## 58: PKD1L1 solid Rest 4 of 14 2 of 43
## 59: THSD7A solid Rest 4 of 14 2 of 43
## 60: VPS13B acinar Rest 1 of 26 8 of 31
## 61: ZNF536 acinar Rest 1 of 26 8 of 31
## 62: ADAMTS20 acinar Rest 1 of 26 8 of 31
## 63: COL6A3 acinar Rest 1 of 26 8 of 31
## 64: FAT4 acinar Rest 1 of 26 8 of 31
## 65: DGKI acinar Rest 1 of 26 8 of 31
## 66: KEAP1 papillary Rest 3 of 6 5 of 51
## 67: CTNND2 solid Rest 5 of 14 4 of 43
## 68: HMCN2 solid Rest 5 of 14 4 of 43
## 69: VPS13B solid Rest 5 of 14 4 of 43
## 70: COL6A3 solid Rest 5 of 14 4 of 43
## 71: DGKI solid Rest 5 of 14 4 of 43
## 72: PKHD1L1 micropapillary Rest 3 of 7 4 of 50
## 73: MUC3A micropapillary Rest 3 of 7 4 of 50
## 74: ADAMTS20 papillary Rest 3 of 6 6 of 51
## Hugo_Symbol Group1 Group2 n_mutated_group1 n_mutated_group2
## p_value OR OR_low OR_high fdr
## 1: 9.112682e-05 37.84731092 3.991610776 1909.7571373 0.09240259
## 2: 1.095098e-03 0.09270694 0.009091654 0.4818028 0.45517130
## 3: 1.732188e-03 14.31983532 2.102947979 169.6342488 0.45517130
## 4: 2.455037e-03 21.57334820 2.079276821 1120.1578249 0.45517130
## 5: 2.588198e-03 0.00000000 0.000000000 0.4975338 0.45517130
## 6: 2.693321e-03 18.64859301 2.157445266 205.3771129 0.45517130
## 7: 4.478455e-03 9.44023459 1.627744533 70.9908140 0.45617315
## 8: 4.478455e-03 9.44023459 1.627744533 70.9908140 0.45617315
## 9: 5.132332e-03 13.99157827 1.741541318 135.0781052 0.45617315
## 10: 5.719520e-03 0.00000000 0.000000000 0.5969768 0.45617315
## 11: 7.339149e-03 10.72219374 1.479698932 129.6610724 0.45617315
## 12: 7.339149e-03 10.72219374 1.479698932 129.6610724 0.45617315
## 13: 7.339149e-03 10.72219374 1.479698932 129.6610724 0.45617315
## 14: 7.643077e-03 0.08711217 0.001868086 0.7010832 0.45617315
## 15: 7.643077e-03 0.08711217 0.001868086 0.7010832 0.45617315
## 16: 8.795827e-03 11.12131460 1.450631913 100.2633539 0.45617315
## 17: 9.627704e-03 6.97278498 1.317966294 42.3117118 0.45617315
## 18: 1.183212e-02 0.13643416 0.013302517 0.7247362 0.45617315
## 19: 1.243401e-02 0.00000000 0.000000000 0.7319136 0.45617315
## 20: 1.332626e-02 5.61133142 1.304302871 26.3072872 0.45617315
## 21: 1.483259e-02 8.43880117 1.188600998 100.1107290 0.45617315
## 22: 1.553126e-02 0.10115754 0.002152104 0.8305514 0.45617315
## 23: 1.553126e-02 0.10115754 0.002152104 0.8305514 0.45617315
## 24: 1.668408e-02 7.06058247 1.141058515 54.1810940 0.45617315
## 25: 1.668408e-02 7.06058247 1.141058515 54.1810940 0.45617315
## 26: 1.668408e-02 7.06058247 1.141058515 54.1810940 0.45617315
## 27: 1.746912e-02 4.86689286 1.152659066 22.2327873 0.45617315
## 28: 1.817327e-02 5.47738734 1.099107756 29.3982865 0.45617315
## 29: 1.817327e-02 5.47738734 1.099107756 29.3982865 0.45617315
## 30: 2.011483e-02 10.82851627 1.099157081 113.1606494 0.45617315
## 31: 2.011483e-02 10.82851627 1.099157081 113.1606494 0.45617315
## 32: 2.020202e-02 7.57039468 1.074438284 89.3371864 0.45617315
## 33: 2.242488e-02 0.22678515 0.045851352 0.8955596 0.45617315
## 34: 2.465971e-02 4.26767929 1.026024439 19.0908509 0.45617315
## 35: 2.663427e-02 0.00000000 0.000000000 0.9251826 0.45617315
## 36: 2.663427e-02 0.00000000 0.000000000 0.9251826 0.45617315
## 37: 2.663427e-02 0.00000000 0.000000000 0.9251826 0.45617315
## 38: 2.663427e-02 0.00000000 0.000000000 0.9251826 0.45617315
## 39: 2.663427e-02 0.00000000 0.000000000 0.9251826 0.45617315
## 40: 2.663427e-02 0.00000000 0.000000000 0.9251826 0.45617315
## 41: 2.701395e-02 4.80038030 1.014565736 31.4180299 0.45617315
## 42: 2.720528e-02 4.96068258 1.111485949 23.4449711 0.45617315
## 43: 2.720528e-02 4.96068258 1.111485949 23.4449711 0.45617315
## 44: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 45: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 46: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 47: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 48: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 49: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 50: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 51: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 52: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 53: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 54: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 55: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 56: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 57: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 58: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 59: 2.736401e-02 7.79869341 0.966262240 97.7488781 0.45617315
## 60: 3.077009e-02 0.11869263 0.002499335 1.0004947 0.45617315
## 61: 3.077009e-02 0.11869263 0.002499335 1.0004947 0.45617315
## 62: 3.077009e-02 0.11869263 0.002499335 1.0004947 0.45617315
## 63: 3.077009e-02 0.11869263 0.002499335 1.0004947 0.45617315
## 64: 3.077009e-02 0.11869263 0.002499335 1.0004947 0.45617315
## 65: 3.077009e-02 0.11869263 0.002499335 1.0004947 0.45617315
## 66: 3.077679e-02 8.60369168 0.912225806 84.1612977 0.45617315
## 67: 3.194112e-02 5.21145581 0.921403533 32.2038762 0.45617315
## 68: 3.194112e-02 5.21145581 0.921403533 32.2038762 0.45617315
## 69: 3.194112e-02 5.21145581 0.921403533 32.2038762 0.45617315
## 70: 3.194112e-02 5.21145581 0.921403533 32.2038762 0.45617315
## 71: 3.194112e-02 5.21145581 0.921403533 32.2038762 0.45617315
## 72: 3.318096e-02 8.08275241 0.882293807 71.9160436 0.46089718
## 73: 3.318096e-02 8.08275241 0.882293807 71.9160436 0.46089718
## 74: 4.412238e-02 7.08910525 0.774798722 66.6306331 0.54820713
## p_value OR OR_low OR_high fdr
Oncogenic Signaling Pathways
## Pathway N n_affected_genes fraction_affected Mutated_samples
## 1: NRF2 3 1 0.3333333 8
## 2: TP53 6 4 0.6666667 21
## 3: TGF-Beta 7 5 0.7142857 4
## 4: MYC 13 6 0.4615385 10
## 5: Cell_Cycle 15 7 0.4666667 6
## 6: PI3K 29 14 0.4827586 17
## 7: Hippo 38 23 0.6052632 30
## 8: WNT 68 30 0.4411765 22
## 9: NOTCH 71 38 0.5352113 29
## 10: RTK-RAS 85 50 0.5882353 47
## Fraction_mutated_samples
## 1: 0.14035088
## 2: 0.36842105
## 3: 0.07017544
## 4: 0.17543860
## 5: 0.10526316
## 6: 0.29824561
## 7: 0.52631579
## 8: 0.38596491
## 9: 0.50877193
## 10: 0.82456140
Clinical enrichment analysis (by aggressiveness)
## Sample size per factor in n_op2:##
## agg ind int
## 36 5 16## Hugo_Symbol Group1 Group2 n_mutated_group1 n_mutated_group2 p_value
## 1: CTNND2 agg Rest 9 of 36 0 of 21 0.01945423
## 2: APOB agg Rest 8 of 36 0 of 21 0.02096930
## 3: ADAMTS12 agg Rest 8 of 36 0 of 21 0.02096930
## 4: PRDM9 agg Rest 8 of 36 0 of 21 0.02096930
## 5: NPAP1 agg Rest 8 of 36 0 of 21 0.02096930
## 6: SORCS1 agg Rest 8 of 36 0 of 21 0.02096930
## 7: CSMD3 int Rest 1 of 16 16 of 41 0.02216306
## 8: ADGRB3 agg Rest 7 of 36 0 of 21 0.03940250
## 9: DCHS2 agg Rest 7 of 36 0 of 21 0.03940250
## 10: LRRTM4 agg Rest 7 of 36 0 of 21 0.03940250
## 11: PTPRC agg Rest 7 of 36 0 of 21 0.03940250
## 12: UNC13B agg Rest 7 of 36 0 of 21 0.03940250
## 13: CACNA1E agg Rest 11 of 36 1 of 21 0.03985523
## 14: OBSCN agg Rest 10 of 36 1 of 21 0.04113546
## 15: CTNND2 int Rest 0 of 16 9 of 41 0.04953378
## 16: CNTNAP4 int Rest 0 of 16 9 of 41 0.04953378
## OR OR_low OR_high fdr
## 1: Inf 1.328554223 Inf 0.946737
## 2: Inf 1.114985573 Inf 0.946737
## 3: Inf 1.114985573 Inf 0.946737
## 4: Inf 1.114985573 Inf 0.946737
## 5: Inf 1.114985573 Inf 0.946737
## 6: Inf 1.114985573 Inf 0.946737
## 7: 0.1073769 0.002336399 0.8338525 0.946737
## 8: Inf 0.915476308 Inf 0.946737
## 9: Inf 0.915476308 Inf 0.946737
## 10: Inf 0.915476308 Inf 0.946737
## 11: Inf 0.915476308 Inf 0.946737
## 12: Inf 0.915476308 Inf 0.946737
## 13: 8.5420267 1.073296253 396.5505636 0.946737
## 14: 7.4804942 0.924818360 349.5846230 0.946737
## 15: 0.0000000 0.000000000 1.1814139 0.946737
## 16: 0.0000000 0.000000000 1.1814139 0.946737
# Comparing groups (separate MAFs)
## -subsetting by clinical data..## --5 samples meet the clinical query## -subsetting by clinical data..## --16 samples meet the clinical query## -subsetting by clinical data..## --36 samples meet the clinical queryIndolent vs Aggressive
| Hugo_Symbol | Indolent | Aggressive | pval | or | ci.up | ci.low | adjPval |
|---|---|---|---|---|---|---|---|
| TTN | 0 | 14 | 0.1464629 | 0.0000000 | 2.018898 | 0.0000000 | 1 |
| DNAH5 | 2 | 5 | 0.1955036 | 3.9411355 | 44.918622 | 0.2672986 | 1 |
| EGFR | 2 | 5 | 0.1955036 | 3.9411355 | 44.918622 | 0.2672986 | 1 |
| RYR3 | 2 | 5 | 0.1955036 | 3.9411355 | 44.918622 | 0.2672986 | 1 |
| ANK2 | 2 | 6 | 0.2464672 | 3.2097811 | 35.157183 | 0.2234139 | 1 |
| CACNA1E | 0 | 11 | 0.2997646 | 0.0000000 | 2.956327 | 0.0000000 | 1 |
| USH2A | 0 | 11 | 0.2997646 | 0.0000000 | 2.956327 | 0.0000000 | 1 |
| OBSCN | 0 | 10 | 0.3102130 | 0.0000000 | 3.408577 | 0.0000000 | 1 |
| RYR2 | 3 | 11 | 0.3169517 | 3.2975734 | 44.753434 | 0.3292036 | 1 |
| ADAMTS12 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| APOB | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| MUC12 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| NPAP1 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| OVCH1 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| PCDH15 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| PCLO | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| PRDM9 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| RELN | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| SORCS1 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| ZNF536 | 0 | 8 | 0.5631694 | 0.0000000 | 4.703327 | 0.0000000 | 1 |
| AHNAK2 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| ANK3 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| CACNA1C | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| COL6A5 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| CUBN | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| FBN2 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| HSPG2 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| KEAP1 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| MUC3A | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| MXRA5 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| NCKAP5 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| PEG3 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| PTPRD | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| SLITRK3 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| SPATA31D1 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| SPTBN4 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| TMEM132B | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| TRPC5 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| ZNF479 | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| ZNF804A | 1 | 5 | 0.5668096 | 1.5315061 | 20.682565 | 0.0262792 | 1 |
| ADGRB3 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| CDH2 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| COL6A3 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| DCHS2 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| ICE1 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| LRRTM4 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| PAPPA2 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| PTPRC | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| RBM10 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| SLITRK2 | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| UNC13B | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| VPS13B | 0 | 7 | 0.5668096 | 0.0000000 | 5.678487 | 0.0000000 | 1 |
| CTNND2 | 0 | 9 | 0.5681334 | 0.0000000 | 3.974876 | 0.0000000 | 1 |
| ADGRL3 | 2 | 8 | 0.5801297 | 2.2779952 | 23.803332 | 0.1638122 | 1 |
| XIRP2 | 2 | 9 | 0.5977371 | 1.9626143 | 20.205003 | 0.1426448 | 1 |
| FLG | 2 | 10 | 0.6196787 | 1.7082681 | 17.388165 | 0.1252037 | 1 |
| MUC16 | 1 | 14 | 0.6357076 | 0.4008352 | 4.623071 | 0.0074587 | 1 |
| LRP1B | 2 | 11 | 0.6448149 | 1.4990570 | 15.123036 | 0.1105846 | 1 |
| ABCA13 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| ADAMTS20 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| BRINP3 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| CACNA1I | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| CADM3 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| CCDC168 | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| CSMD2 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| CSMD3 | 2 | 14 | 1.0000000 | 1.0464010 | 10.385608 | 0.0781803 | 1 |
| DGKI | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| DNAH8 | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| EGFLAM | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| EPHA3 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| EYS | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| FAT2 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| FAT3 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| FAT4 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| FSIP2 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| HMCN1 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| HMCN2 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| IGFN1 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| KCNT2 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| KIAA1109 | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| KNDC1 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| LRP2 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| MALRD1 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| MGAM | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| MGAM2 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| MROH2B | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| MTUS2 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| MUC17 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| MUC5B | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| MYH2 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| OTOGL | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| PKHD1L1 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| PXDNL | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| SI | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| SPTA1 | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| STAB2 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| TENM3 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| THSD7A | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| TP53 | 1 | 11 | 1.0000000 | 0.5753117 | 6.760275 | 0.0105936 | 1 |
| TPTE | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| TSHZ3 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| UNC79 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| VCAN | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| WDFY4 | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| ZFHX4 | 1 | 12 | 1.0000000 | 0.5076059 | 5.918500 | 0.0093877 | 1 |
| ZFPM2 | 1 | 7 | 1.0000000 | 1.0348233 | 12.930454 | 0.0184306 | 1 |
| ZNF423 | 1 | 6 | 1.0000000 | 1.2428269 | 16.023515 | 0.0217935 | 1 |
| ZNF729 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| ZNF831 | 0 | 6 | 1.0000000 | 0.0000000 | 7.048622 | 0.0000000 | 1 |
| ADGRV1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ALPK1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ALPK3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ARID1A | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ARPP21 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ASB15 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ASTN1 | 1 | 10 | 1.0000000 | 0.6563176 | 7.788950 | 0.0120189 | 1 |
| ASTN2 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ASXL3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ATP1A4 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| BIRC6 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| C6orf132 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CA9 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CACNA2D1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CD163 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CDH12 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CFHR5 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CNTNAP4 | 1 | 8 | 1.0000000 | 0.8777738 | 10.727789 | 0.0158209 | 1 |
| CNTNAP5 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| COL12A1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| COL22A1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| COL2A1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| COL3A1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| COL4A5 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CRYBG2 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| CSMD1 | 1 | 9 | 1.0000000 | 0.7550003 | 9.074672 | 0.0137296 | 1 |
| DGKB | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| DNAH10 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| DNAH11 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| DNAH3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| DNAH7 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| DST | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| EDIL3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ERICH3 | 1 | 9 | 1.0000000 | 0.7550003 | 9.074672 | 0.0137296 | 1 |
| FCGBP | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| KCNH7 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| KCP | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| KRAS | 2 | 15 | 1.0000000 | 0.9348824 | 9.249026 | 0.0700072 | 1 |
| KRBA1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| LAMA1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| LRRC7 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| MROH2A | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| MYH4 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| MYH6 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| NAV3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| NBAS | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| NEB | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| NELL1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| NRXN1 | 1 | 10 | 1.0000000 | 0.6563176 | 7.788950 | 0.0120189 | 1 |
| NXF5 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| OR2T2 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| PKD1L1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| PLXNA4 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| POTEA | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| POU3F3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| PPFIA2 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| RIMBP2 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| RP1L1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| RYR1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| SALL3 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| SCN3A | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| TIAM1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| TMEM132C | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| TNN | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ZEB1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| ZIC1 | 0 | 5 | 1.0000000 | 0.0000000 | 9.119767 | 0.0000000 | 1 |
| Cohort | SampleSize |
|---|---|
| Indolent | 5 |
| Aggressive | 36 |
Indolent+Intermediate vs Aggressive
## -subsetting by clinical data..## --21 samples meet the clinical query## -subsetting by clinical data..## --36 samples meet the clinical query| Hugo_Symbol | Indolent + Int | Aggressive | pval | or | ci.up | ci.low | adjPval |
|---|---|---|---|---|---|---|---|
| CTNND2 | 0 | 9 | 0.0194542 | 0.0000000 | 0.7526979 | 0.0000000 | 0.3846968 |
| ADAMTS12 | 0 | 8 | 0.0209693 | 0.0000000 | 0.8968726 | 0.0000000 | 0.3846968 |
| APOB | 0 | 8 | 0.0209693 | 0.0000000 | 0.8968726 | 0.0000000 | 0.3846968 |
| NPAP1 | 0 | 8 | 0.0209693 | 0.0000000 | 0.8968726 | 0.0000000 | 0.3846968 |
| PRDM9 | 0 | 8 | 0.0209693 | 0.0000000 | 0.8968726 | 0.0000000 | 0.3846968 |
| SORCS1 | 0 | 8 | 0.0209693 | 0.0000000 | 0.8968726 | 0.0000000 | 0.3846968 |
| ADGRB3 | 0 | 7 | 0.0394025 | 0.0000000 | 1.0923276 | 0.0000000 | 0.3846968 |
| DCHS2 | 0 | 7 | 0.0394025 | 0.0000000 | 1.0923276 | 0.0000000 | 0.3846968 |
| LRRTM4 | 0 | 7 | 0.0394025 | 0.0000000 | 1.0923276 | 0.0000000 | 0.3846968 |
| PTPRC | 0 | 7 | 0.0394025 | 0.0000000 | 1.0923276 | 0.0000000 | 0.3846968 |
| UNC13B | 0 | 7 | 0.0394025 | 0.0000000 | 1.0923276 | 0.0000000 | 0.3846968 |
| CACNA1E | 1 | 11 | 0.0398552 | 0.1170682 | 0.9317092 | 0.0025217 | 0.3846968 |
| OBSCN | 1 | 10 | 0.0411355 | 0.1336810 | 1.0812934 | 0.0028605 | 0.3846968 |
| ZFHX4 | 2 | 12 | 0.0584136 | 0.2156646 | 1.1514147 | 0.0209878 | 0.3846968 |
| CSMD3 | 3 | 14 | 0.0725792 | 0.2677393 | 1.1764364 | 0.0427106 | 0.3846968 |
| CSMD2 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| EGFLAM | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| EPHA3 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| IGFN1 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| MGAM2 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| MROH2B | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| PXDNL | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| TENM3 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| THSD7A | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| TPTE | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| TSHZ3 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| UNC79 | 0 | 6 | 0.0753583 | 0.0000000 | 1.3720598 | 0.0000000 | 0.3846968 |
| EGFR | 7 | 5 | 0.1018339 | 3.0333470 | 14.4652194 | 0.6913165 | 0.3846968 |
| CNTNAP4 | 1 | 8 | 0.1331558 | 0.1792817 | 1.5206016 | 0.0037643 | 0.3846968 |
| PCLO | 1 | 8 | 0.1331558 | 0.1792817 | 1.5206016 | 0.0037643 | 0.3846968 |
| ZNF536 | 1 | 8 | 0.1331558 | 0.1792817 | 1.5206016 | 0.0037643 | 0.3846968 |
| ALPK1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| ARPP21 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| ASB15 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| ATP1A4 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| C6orf132 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| CA9 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| CACNA2D1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| CD163 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| CDH12 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| CFHR5 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| CNTNAP5 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| COL12A1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| COL22A1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| COL2A1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| COL4A5 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| DGKB | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| DNAH10 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| DNAH3 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| DST | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| EDIL3 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| KCP | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| KRBA1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| LRRC7 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| MROH2A | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| MYH4 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| NEB | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| NELL1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| NXF5 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| OR2T2 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| POTEA | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| POU3F3 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| PPFIA2 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| RIMBP2 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| RYR1 | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| SCN3A | 0 | 5 | 0.1463543 | 0.0000000 | 1.8040200 | 0.0000000 | 0.3846968 |
| MUC16 | 4 | 14 | 0.1486329 | 0.3760077 | 1.4955896 | 0.0760950 | 0.3846968 |
| TTN | 4 | 14 | 0.1486329 | 0.3760077 | 1.4955896 | 0.0760950 | 0.3846968 |
| ASTN1 | 2 | 10 | 0.1773045 | 0.2792342 | 1.5390316 | 0.0267534 | 0.4457941 |
| NRXN1 | 2 | 10 | 0.1773045 | 0.2792342 | 1.5390316 | 0.0267534 | 0.4457941 |
| CSMD1 | 2 | 9 | 0.1854077 | 0.3215125 | 1.8126233 | 0.0305038 | 0.4532188 |
| ERICH3 | 2 | 9 | 0.1854077 | 0.3215125 | 1.8126233 | 0.0305038 | 0.4532188 |
| LRP1B | 3 | 11 | 0.2137720 | 0.3848555 | 1.7530604 | 0.0602898 | 0.4797555 |
| CDH2 | 1 | 7 | 0.2356734 | 0.2117815 | 1.8614334 | 0.0043859 | 0.4797555 |
| DNAH8 | 1 | 7 | 0.2356734 | 0.2117815 | 1.8614334 | 0.0043859 | 0.4797555 |
| PAPPA2 | 1 | 7 | 0.2356734 | 0.2117815 | 1.8614334 | 0.0043859 | 0.4797555 |
| SLITRK2 | 1 | 7 | 0.2356734 | 0.2117815 | 1.8614334 | 0.0043859 | 0.4797555 |
| WDFY4 | 1 | 7 | 0.2356734 | 0.2117815 | 1.8614334 | 0.0043859 | 0.4797555 |
| ZFPM2 | 1 | 7 | 0.2356734 | 0.2117815 | 1.8614334 | 0.0043859 | 0.4797555 |
| CADM3 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| HMCN1 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| KCNT2 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| LRP2 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| MGAM | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| MUC5B | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| PKHD1L1 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| STAB2 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| ZNF729 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| ZNF831 | 1 | 6 | 0.2426036 | 0.2550261 | 2.3544444 | 0.0051855 | 0.4797555 |
| TENM1 | 5 | 4 | 0.2663924 | 2.4572820 | 14.2260245 | 0.4589171 | 0.5209451 |
| MUC12 | 2 | 8 | 0.2952934 | 0.3742905 | 2.1728706 | 0.0350259 | 0.5649091 |
| OVCH1 | 2 | 8 | 0.2952934 | 0.3742905 | 2.1728706 | 0.0350259 | 0.5649091 |
| RYR2 | 9 | 11 | 0.3973204 | 1.6882593 | 5.9817925 | 0.4778288 | 0.6190044 |
| ALPK3 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| ANK3 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| ARID1A | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| ASTN2 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| CACNA1C | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| COL3A1 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| COL6A5 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| CRYBG2 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| FCGBP | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| KCNH7 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| MYH6 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| NBAS | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| PKD1L1 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| PLXNA4 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| RP1L1 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| SALL3 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| TMEM132B | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| ZEB1 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| ZIC1 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| ZNF479 | 1 | 5 | 0.3974290 | 0.3154090 | 3.1267166 | 0.0062521 | 0.6190044 |
| COL6A3 | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| DGKI | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| ICE1 | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| KIAA1109 | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| RBM10 | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| SPTA1 | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| VPS13B | 2 | 7 | 0.4612482 | 0.4419318 | 2.6677534 | 0.0406451 | 0.6764973 |
| RYR3 | 5 | 5 | 0.4729422 | 1.9139979 | 9.7078377 | 0.3795817 | 0.6879159 |
| XIRP2 | 3 | 9 | 0.5037717 | 0.5057722 | 2.4044101 | 0.0775279 | 0.7267527 |
| FLG | 4 | 10 | 0.5376305 | 0.6168900 | 2.5968468 | 0.1211591 | 0.7692925 |
| ABCA13 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| BRINP3 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| CACNA1I | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| EYS | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| FSIP2 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| KNDC1 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| MALRD1 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| MTUS2 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| MYH2 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| SI | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| ZNF423 | 2 | 6 | 0.6965651 | 0.5318590 | 3.3878174 | 0.0478025 | 0.9148914 |
| ADGRL3 | 3 | 8 | 0.7292230 | 0.5886169 | 2.8863169 | 0.0888244 | 0.9243717 |
| PCDH15 | 3 | 8 | 0.7292230 | 0.5886169 | 2.8863169 | 0.0888244 | 0.9243717 |
| RELN | 3 | 8 | 0.7292230 | 0.5886169 | 2.8863169 | 0.0888244 | 0.9243717 |
| CCDC168 | 3 | 7 | 0.7300435 | 0.6948259 | 3.5505425 | 0.1028103 | 0.9243717 |
| VCAN | 3 | 7 | 0.7300435 | 0.6948259 | 3.5505425 | 0.1028103 | 0.9243717 |
| TP53 | 5 | 11 | 0.7617846 | 0.7144253 | 2.7724814 | 0.1628221 | 0.9508801 |
| USH2A | 5 | 11 | 0.7617846 | 0.7144253 | 2.7724814 | 0.1628221 | 0.9508801 |
| DNAH5 | 3 | 5 | 1.0000000 | 1.0327617 | 6.0589848 | 0.1433700 | 1.0000000 |
| KEAP1 | 3 | 5 | 1.0000000 | 1.0327617 | 6.0589848 | 0.1433700 | 1.0000000 |
| KRAS | 9 | 15 | 1.0000000 | 1.0490724 | 3.5504102 | 0.3047852 | 1.0000000 |
| LAMA1 | 3 | 5 | 1.0000000 | 1.0327617 | 6.0589848 | 0.1433700 | 1.0000000 |
| MXRA5 | 3 | 5 | 1.0000000 | 1.0327617 | 6.0589848 | 0.1433700 | 1.0000000 |
| SPATA31D1 | 3 | 5 | 1.0000000 | 1.0327617 | 6.0589848 | 0.1433700 | 1.0000000 |
| ADAMTS20 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| ADGRV1 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| AHNAK2 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| ANK2 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| ASXL3 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| BIRC6 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| CUBN | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| DNAH11 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| DNAH7 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| FAT2 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| FAT3 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| FAT4 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| FBN2 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| HMCN2 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| HSPG2 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| MUC17 | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| MUC3A | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| NAV3 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| NCKAP5 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| OTOGL | 3 | 6 | 1.0000000 | 0.8359613 | 4.5204359 | 0.1203777 | 1.0000000 |
| PEG3 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| PTPRD | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| SLITRK3 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| SPTBN4 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| TIAM1 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| TMEM132C | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| TNN | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| TRPC5 | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| ZNF804A | 2 | 5 | 1.0000000 | 0.6573022 | 4.5246559 | 0.0572104 | 1.0000000 |
| Cohort | SampleSize |
|---|---|
| Indolent + Int | 21 |
| Aggressive | 36 |
